[AMBER] Fw: Average number of water molecules per GIST group

From: Miroslav Dikov via AMBER <amber.ambermd.org>
Date: Wed, 20 Jul 2022 10:52:23 +0000 (UTC)

Dear AMBER users,
Recently I started using GIST as implemented in CPPTRAJ and gistpp, for which I have been following the main tutorial at the AMBER website. However, I am still not clear on how to obtain the average number of water molecules per group as generated by “gistpp <…> -op group”. 
One of the files generated by gist is called grcount.txt and at first sight it seems that it outputs the average number of molecules per group, but this is not the case, because the resulting values are too high (~90 for a single water molecule in the binding site). If I normalise against the length of the trajectory (1000 frames), then the values become too low (0.09 molecules, which is again not consistent with visually inspecting the trajectory).
Does anyone have experience obtaining the average number of water molecules per GIST group? Any help would be much appreciated.
Kind regards,Miro
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Received on Thu Aug 04 2022 - 13:35:02 PDT
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